ELECTRON MICROSCOPY

Sample

NAIP5-NLRC4-flagellin inflammasome

Specimen Preperation
Sample Aggregation State PARTICLE
Vitrification Instrument FEI VITROBOT MARK II
Cryogen Name ETHANE
Sample Vitrification Details ?
3D Reconstruction
Reconstruction Method SINGLE PARTICLE
Number of Particles 252214
Reported Resolution (Å) 5.2
Resolution Method FSC 0.143 CUT-OFF
Other Details ?
Refinement Type
Symmetry Type POINT
Map-Model Fitting and Refinement
ID 1
Refinement Space REAL
Refinement Protocol FLEXIBLE FIT
Refinement Target Correlation coefficient
Overall B Value 167
Fitting Procedure ?
Details Homology models predicted by I-TASSER server were used as initial model sources. The main structural template identified by I-TASSER for NAIP5 was the crystal structure of NLRC4 in the inactive conformation (PDB ID: 4KXF) that covered all the domains except the N-terminal BIR region, where homology models from several BIR domains were recognized (PDB IDs: 1SE0, 2VM5, and 1OXQ for BIR1, BIR2, and BIR3, respectively). Predictions were first rigid body docked into the density map using Chimera and/or ADP_EM. Then, the docked models were flexibly fitted with iMODFIT, if necessary. Finally, all models were refined in Phenix.
Data Acquisition
Detector Type GATAN K2 SUMMIT (4k x 4k)
Electron Dose (electrons/Å2) 45.8
Imaging Experiment
Date of Experiment ?
Temprature (Kelvin)
Microscope Model FEI TITAN KRIOS
Minimum Defocus (nm) 1800
Maximum Defocus (nm) 4000
Minimum Tilt Angle (degrees) ?
Maximum Tilt Angle (degrees) ?
Nominal CS ?
Imaging Mode BRIGHT FIELD
Specimen Holder Model ?
Nominal Magnification 22500
Calibrated Magnification ?
Source FIELD EMISSION GUN
Acceleration Voltage (kV) 300
Imaging Details ?
Imaging Experiment
Task Software Package Version
PARTICLE SELECTION RELION 1.4
IMAGE ACQUISITION SerialEM ?
CTF CORRECTION Gctf 0.5
MODEL FITTING UCSF Chimera 1.10.1
MODEL FITTING ADP_EM 1.21
MODEL FITTING iMODFIT 1.45
INITIAL EULER ASSIGNMENT EMAN2 2.05
FINAL EULER ASSIGNMENT RELION 1.4
CLASSIFICATION RELION 1.4
RECONSTRUCTION RELION 1.4
MODEL REFINEMENT PHENIX 1.11.1-2575
MODEL REFINEMENT I-TASSER 5.1
Image Processing
CTF Correction Type CTF Correction Details Number of Particles Selected Particle Selection Details
PHASE FLIPPING AND AMPLITUDE CORRECTION ?
Feedback Form
Name
Email
Institute
Feedback